A number of inherited genetic diseases and types of cancer have been linked to chromosomal translocation events which result in the fusion of two genes which do not occur together in the normal genome. Certain conditions involve translocations which frequently occur at the same or very near location. The chromosome regions where frequent breaks occur are called breakpoint regions.
One of the best known examples of a clinically important translocation is the Philadelphia Chromosome which results from a break in the ABL1 gene on distal chromosome 9q and the BCR gene on proximal chromosome 22q {t(9;22)} (FIG. 1). The breakpoints within the ABL1 gene may occur throughout a region spanning more than 175 kb upstream from exon II while the breaks in chromosome 22 are clustered into two areas of the BCR gene, termed the major breakpoint cluster region (m-bcr) and the minor breakpoint cluster region (M-bcr) (Kurzrock et al, New England Journal of Medicine, 319:990 (1988)). The Philadelphia Chromosome occurs in most cases of Chronic Myelogenous Leukemia (CML) and some cases of Acute Lymphocytic Leukemia (ALL). Other important translocations include, but are not limited to, t(8;21) in Acute Myelogenous Leukemia, t(8:14) in Burkett's Lymphoma and pre-B-cell Acute Lymphoblastic Leukemia, t(1:14), t(7:9), t(7:19), t(11:14), t(10:14) and t(7:9) in T-acute Lymphoblastic Leukemia, t(15;17) in Acute Myelogenous Leukemia (AML) and t(15:17) Acute Promyelocytic Leukemia (PML). Solid tumors include, t(9;22) in Ewing's Sarcoma, t(15:16), and hereditary diseases associated with translocations include a number of mental retardation associated syndromes. It is likely that other conditions are caused by subcriptic translocations or other structural aberrations which are yet to be determined and are too small to be noticed by standard cytogenetics.
Multiple genetic testing methods have been developed for use in diagnosis, monitoring of minimal residual disease and/or response to therapy during clinical practice. However, no single technique has been developed that can accurately detect and quantify disease at diagnosis and throughout treatment. Conventional quantitative cytogenetics and G-banding analysis is cumbersome and can only be applied to cycling cells (Lion, Leukemia 10: 896 (1996)). In practice, the sensitivity of conventional cytogenetics is dependent upon the number of good metaphase cells which can be evaluated. In the example of cancers caused by neoplastic cells in the bone marrow, obtaining large numbers of good metaphase cells from bone marrows of patients is difficult.
More recently, the assay technique in situ hybridization (ISH), particularly fluorescent in situ hybridization (FISH) (Pinkel et al, Proc. Natl. Acad. Sci., U.S.A. 83:2934–2938 (1986)) has been of assistance in detecting translocations. FISH allows the analysis of individual metaphase or interphase cells, thereby eliminating the need to obtain and assay cycling cells. It is therefore possible to use nondividing tissue, including bone marrow and peripheral blood cells in a diagnostic or prognostic analysis.
In the field of detecting the Philadelphia Chromosome, a commonly used method for detection of ABL1/BCR fusion utilizes differently labeled probes for BCR and ABL1, and detects a single ABL1/BCR fusion (or closely linked) signal in cells with a Ph chromosome. (This method is referred to for convenience as S-FISH.) An example of this technique is Tkachuk et al, Science 205: p. 559–562 (1990) where one fluorescently labeled probe hybridized to part of the ABL1 gene and a second fluorescently labeled probe hybridized to part of the BCR gene.
The probes in commercial single FISH test kits do not span the entire length of each translocation breakpoint but rather are designed to bind to one portion of each gene, i.e. sometimes overlapping or adjacent to a breakpoint region, sometimes many kilobases away and sometimes both (See FIG. 1 of Tkachuk et al for example). Normal chromosomes 9 and 22 each bind one probe, which is specific to that chromosome. The Philadelphia Chromosome, both probes hybridize at the fusion site bringing both labels in close proximity so as to usually form a color shift or fusion near proximity/signal. Because the exact breakpoint may vary, the two probe labels may not come sufficiently close to form a fusion label. Likewise for probes useable to detect the t(8;21) translocation in Acute Myelogenous Leukemia (AML).
Using the probe configuration above, the following detection method-for the Philadelphia Chromosome using FISH has been used: the ABL1 gene probe is labeled using a probe containing one hapten or fluorophore (for example, FITC) and the BCR gene probe is labeled using a probe containing another hapten or fluorophore (for example Rhodamine). After hybridization and detection, a normal chromosome 9 shows the green signal and a normal chromosome 22 shows a red signal. A normal cell would therefore exhibit two red signals and two green signals. A cell containing a Philadelphia chromosome has one red and one green signal for the unaffected homologues of chromosomes 9 and 22 and one white, yellow or closely linked pair of signals that results from the close proximity of the labeled probes hybridized to the translocated BCR and ABL1 genes, the so-called fusion signal.
However, the probes used heretofore in this method have not been constructed so as to specifically bind and detect the second fusion site for the reciprocal translocation event. Thus, the S-FISH method detects only one of the abnormal chromosomes resulting from the translocation event, the Philadelphia chromosome.
In another method using labelled probes to detect ALL gene rearrangements in solid tumors, a probe set was designed so that the two probes lie adjacent to each other on the normal chromosome, but split apart and move to the two different abnormal chromosomes if the translocation has occurred (Croce, U.S. Pat. No. 5,567,586, hereby incorporated by reference). In this method the probes are designed to be complementary to sequences in the translocation region on one chromosome. In this method, the fluorescent probes produce a single spot on the normal chromosome, but appear as two distinct spots when translocation has occurred.
The same format has been used for other assays for detecting other translocations such as t(8:21) in Acute Myeloid Leukemia (AML). For example, Le Beau, Blood 81: 1979–1983 (1993), and Sacchi et al, Cancer Genetics and Cytogenetics 79: 97–103 (1995) and Fischer et al, Blood 88: 3962–3971 (1996).